HEADER DE NOVO PROTEIN 24-AUG-21 5SBJ TITLE THE CRYSTAL STRUCTURE OF METP IN COMPLEX WITH CD AT A RESOLUTION OF TITLE 2 1.29 A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: METP, MINIATURIZED RUBREDOXIN; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.DI COSTANZO,S.LA GATTA,V.PAVONE REVDAT 3 03-APR-24 5SBJ 1 REMARK REVDAT 2 15-NOV-23 5SBJ 1 REMARK REVDAT 1 15-FEB-23 5SBJ 0 JRNL AUTH M.CHINO,L.DI COSTANZO JRNL TITL MINIATURIZATION PROCESS RELOADED - STRUCTURAL AND FUNCTIONAL JRNL TITL 2 INSIGHTS FROM A MINIATURIZED RUBREDOXIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 5466 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.0288 - 1.6130 0.99 2655 134 0.1296 0.1517 REMARK 3 2 1.6130 - 1.2802 0.99 2535 142 0.2243 0.2294 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5SBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1001404300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.010 REMARK 200 RESOLUTION RANGE LOW (A) : 31.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 2.150 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: ROSETTA, COMPUTATIONAL MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 1.4 M SODIUM CITRATE REMARK 280 TRIBASIC DIHYDRATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 9.66550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 9.66550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 18.53500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.32700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.53500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.32700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.66550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.53500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.32700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 9.66550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.53500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 28.32700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP C 25 CB ASP C 25 CG 0.237 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP C 25 CB - CG - OD1 ANGL. DEV. = -35.9 DEGREES REMARK 500 ASP C 25 CB - CG - OD2 ANGL. DEV. = 32.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD C 101 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 2 SG REMARK 620 2 CYS C 5 SG 113.5 REMARK 620 3 CYS C 17 SG 110.5 104.1 REMARK 620 4 CYS C 20 SG 107.8 111.7 109.2 REMARK 620 N 1 2 3 DBREF 5SBJ C 0 29 PDB 5SBJ 5SBJ 0 29 SEQRES 1 C 30 ACE TYR CYS SER ASP CYS GLY ALA ASP AIB SER GLN VAL SEQRES 2 C 30 ARG GLY GLY TYR CYS THR ASN CYS GLY ALA SER AIB ASP SEQRES 3 C 30 ARG ILE ARG NH2 HET ACE C 0 3 HET AIB C 9 13 HET AIB C 24 13 HET NH2 C 29 3 HET CD C 101 1 HETNAM ACE ACETYL GROUP HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM NH2 AMINO GROUP HETNAM CD CADMIUM ION FORMUL 1 ACE C2 H4 O FORMUL 1 AIB 2(C4 H9 N O2) FORMUL 1 NH2 H2 N FORMUL 2 CD CD 2+ FORMUL 3 HOH *21(H2 O) HELIX 1 AA1 ASP C 8 SER C 10 5 3 HELIX 2 AA2 SER C 23 ASP C 25 5 3 SHEET 1 AA1 2 TYR C 1 CYS C 2 0 SHEET 2 AA1 2 ILE C 27 ARG C 28 -1 O ARG C 28 N TYR C 1 SHEET 1 AA2 2 VAL C 12 ARG C 13 0 SHEET 2 AA2 2 TYR C 16 CYS C 17 -1 O TYR C 16 N ARG C 13 LINK C ACE C 0 N TYR C 1 1555 1555 1.34 LINK C ASP C 8 N AIB C 9 1555 1555 1.33 LINK C AIB C 9 N SER C 10 1555 1555 1.33 LINK C SER C 23 N AIB C 24 1555 1555 1.33 LINK C AIB C 24 N ASP C 25 1555 1555 1.35 LINK C ARG C 28 N ANH2 C 29 1555 1555 1.32 LINK SG CYS C 2 CD CD C 101 1555 1555 2.50 LINK SG CYS C 5 CD CD C 101 1555 1555 2.51 LINK SG CYS C 17 CD CD C 101 1555 1555 2.55 LINK SG CYS C 20 CD CD C 101 1555 1555 2.52 CRYST1 37.070 56.654 19.331 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026976 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017651 0.000000 0.00000 SCALE3 0.000000 0.000000 0.051730 0.00000 HETATM 1 C ACE C 0 5.605 5.661 6.616 1.00 11.95 C ANISOU 1 C ACE C 0 2121 1357 1063 -154 -150 -57 C HETATM 2 O ACE C 0 4.604 5.700 7.350 1.00 13.18 O ANISOU 2 O ACE C 0 2228 1486 1295 -165 -161 -6 O HETATM 3 CH3 ACE C 0 5.575 6.097 5.176 1.00 13.87 C ANISOU 3 CH3 ACE C 0 2415 1615 1242 -192 -190 -64 C